061024_ResearchTalks_CgHbProjectors

Slides used for CSHL Statistical Analysis of Genome Scale Data Research talks about the Cg Hb projector neurons profiling using snRNAseq data

Transcript

1. Research talk: Cg Hb cell projectors study CSHL Statistical Analysis of Genome Scale Data Melissa Mayén Quiroz 06/10/2024 https://github.com/Melii99 mmayen@lcg.unam.mx @meli_mq99
2. • Pilot Chromium sn-scRNAseq experiment in which they wanted to tag and capture projector neuron nuclei • 10x genomics Chromium platform and Illumina Next Generation Sequencing • Based on previous histological observations Ege has done, she expects the data of interest from sample 2-Cg-Hb-pos to be indicative of deep-layer cortical projection neurons retrograde AAV injection at the habenula of 7 mice to deliver a GFP reporter
4. • Empty Droplets • Quality Control • Doublet detection • GLM-PCA • Harmony • Clustering • Marker genes • Cell Type markers • Annotation • iSEE shiny app
5. https://libd.shinyapps.io/Hb_Cg_projection_profiling/
6. • Clusters 1,2, and 4 are non-neuronal and group together on the TSNE/UMAP whilst still being distinct. • Clusters 6 and 12 are likely superficial layer excitatory neurons and group together. • Clusters 5 (superficial layer contamination) and 10 are likely deeper layer excitatory neurons, as well as 8, 11 and 13, and they all group together while being distinct. (8 and 11 less clear) • Clusters 3 and 9 are likely to be inhibitory neurons • Cluster 7 I think is a mix of non-neuronal cells, inhibitory neurons and excitatory neurons. (All over the place) The clustering gives a good sense of different cell types, but doesn't get at the finer resolution, even for the non-neuronal cell types. Filtrate non-neuronal populations Sub-clustering Hb_VTA_projector_profiling
7. Thank You!